Accurate, fast and non-destructive identification of varieties of common bean seeds is important for the cultivation and efficient utilization of common beans. This study is based on hyperspectral and deep learning to identify the varieties of common bean seeds non-destructively. In this study, the average spectrum of 3078 hyperspectral images from 500 varieties was obtained after image segmentation and sensitive region extraction, and the Synthetic Minority Over-sampling Technique (SMOTE) was used to achieve the equilibrium of the samples of various varieties. A one-dimensional convolutional neural network model (IResCNN) incorporating Inception module and residual structure was proposed to identify seed varieties, and Support Vector Machine (SVM), K-Nearest Neighbor (KNN), VGG19, AlexNet, ResNet50 were established to compare the identification effect. After analyzing the effects of multiple spectral preprocessing methods on the model, the study selected Savitzky-Golay smoothing correction (SG) for spectral preprocessing and extracted 66 characteristic wavelengths using Successive Projections Algorithm (SPA) as inputs to the discriminative model. Ultimately, the IResCNN model achieved the highest accuracy of 93.06 % on the test set, indicating that hyperspectral technology can accurately identify bean varieties, and the study provides a correct method of thinking for the non-destructive classification of multi-species small-sample bean varieties.